Here's my data of total execution count based on logging PocketNES. It's not comprehensive. Data may be inaccurate, because the emulator has speedhacks, so it tries to skip idle loops. LDA $nn, BNE/BEQ, and JMP are much greater than what is shown here.
If you took out any idle loop parts of a game, the list would be very different.
Code:
7.4797% _A5 LDA $nn
5.7161% _D0 BNE *
5.3027% _85 STA $nn
4.5473% _F0 BEQ *
3.1360% _E8 INX
2.7743% _20 JSR $nnnn
2.7525% _60 RTS
2.7162% _C8 INY
2.6038% _9D STA $nnnn,X
2.5311% _18 CLC
2.5233% _BD LDA $nnnn,X
2.5231% _29 AND #$nn
2.4835% _AD LDA $nnnn
2.2968% _8D STA $nnnn
2.1907% _6E ROR $nnnn
2.1410% _66 ROR $nn
2.1025% _C9 CMP #$nn
2.0923% _4A LSR
2.0549% _10 BPL *
1.7834% _CA DEX
1.7301% _A9 LDA #$nn
1.7259% _B1 LDA ($nn),Y
1.6681% _88 DEY
1.6523% _90 BCC *
1.6431% _65 ADC $nn
1.5062% _4C JMP $nnnn
1.2130% _B0 BCS *
1.1877% _30 BMI *
1.1778% _B9 LDA $nnnn,Y
1.1399% _0A ASL
1.1014% _69 ADC #$nn
0.9876% _38 SEC
0.9143% _EA NOP
0.8458% _C6 DEC $nn
0.8078% _A0 LDY #$nn
0.7783% _45 EOR $nn
0.7761% _B5 LDA $nn,X
0.7436% _99 STA $nnnn,Y
0.7131% _05 ORA $nn
0.7099% _68 PLA
0.7064% _AA TAX
0.6906% _E0 CPX #$nn
0.6371% _A8 TAY
0.6323% _48 PHA
0.6079% _8A TXA
0.5931% _26 ROL $nn
0.5134% _E6 INC $nn
0.5105% _A6 LDX $nn
0.4982% _A4 LDY $nn
0.4661% _E9 SBC #$nn
0.4423% _A2 LDX #$nn
0.4328% _2A ROL
0.4327% _91 STA ($nn),Y
0.4173% _C5 CMP $nn
0.3839% _86 STX $nn
0.3662% _98 TYA
0.3594% _C0 CPY #$nn
0.3493% _E5 SBC $nn
0.3350% _BC LDY $nnnn,X
0.3162% _95 STA $nn,X
0.2551% _2C BIT $nnnn
0.2532% _6A ROR
0.2522% _46 LSR $nn
0.2392% _84 STY $nn
0.2258% _06 ASL $nn
0.2253% _7D ADC $nnnn,X
0.1876% _25 AND $nn
0.1617% _24 BIT $nn
0.1513% _8E STX $nnnn
0.1507% _8C STY $nnnn
0.1490% _70 BVS *
0.1412% _DD CMP $nnnn,X
0.1354% _ED SBC $nnnn
0.1343% _58 CLI
0.1266% _49 EOR #$nn
0.1200% _09 ORA #$nn
0.1122% _F5 SBC $nn,X
0.1083% _AE LDX $nnnn
0.1034% _55 EOR $nn,X
0.1020% _6C JMP ($nnnn)
0.1006% _11 ORA ($nn),Y
0.0985% _6D ADC $nnnn
0.0929% _E4 CPX $nn
0.0891% _C4 CPY $nn
0.0888% _FD SBC $nnnn,X
0.0887% _4D EOR $nnnn
0.0828% _DE DEC $nnnn,X
0.0826% _D9 CMP $nnnn,Y
0.0744% _79 ADC $nnnn,Y
0.0691% _2E ROL $nnnn
0.0668% _50 BVC *
0.0659% _1D ORA $nnnn,X
0.0658% _0D ORA $nnnn
0.0628% _71 ADC ($nn),Y
0.0611% _36 ROL $nn,X
0.0549% _AC LDY $nnnn
0.0533% _19 ORA $nnnn,Y
0.0510% _EC CPX $nnnn
0.0499% _CE DEC $nnnn
0.0479% _31 AND ($nn),Y
0.0456% _28 PLP
0.0456% _08 PHP
0.0425% _B4 LDY $nn,X
0.0404% _CD CMP $nnnn
0.0395% _FE INC $nnnn,X
0.0390% _78 SEI
0.0354% _B6 LDX $nn,Y
0.0344% _D5 CMP $nn,X
0.0344% _75 ADC $nn,X
0.0338% _EE INC $nnnn
0.0326% _40 RTI
0.0313% _2D AND $nnnn
0.0250% _F1 SBC ($nn),Y
0.0232% _BE LDX $nnnn,Y
0.0220% _3D AND $nnnn,X
0.0214% _A1 LDA ($nn,X)
0.0210% _96 STX $nn,Y
0.0158% _4E LSR $nnnn
0.0154% _94 STY $nn,X
0.0147% _0E ASL $nnnn
0.0144% _F6 INC $nn,X
0.0141% _D1 CMP ($nn),Y
0.0137% _F9 SBC $nnnn,Y
0.0129% _35 AND $nn,X
0.0124% _15 ORA $nn,X
0.0114% _D6 DEC $nn,X
0.0095% _BA TSX
0.0092% _CC CPY $nnnn
0.0085% _76 ROR $nn,X
0.0073% _9A TXS
0.0070% _7E ROR $nnnn,X
0.0059% _39 AND $nnnn,Y
0.0030% _51 EOR ($nn),Y
0.0029% _3E ROL $nnnn,X
0.0026% _81 STA ($nn,X)
0.0022% _5D EOR $nnnn,X
0.0015% _1E ASL $nnnn,X
0.0013% _5E LSR $nnnn,X
0.0009% _16 ASL $nn,X
0.0004% _D8 CLD
0.0003% _B8 CLV
0.0003% _59 EOR $nnnn,Y
0.0001% _01 ORA ($nn,X)
0.0000% _C1 CMP ($nn,X)
0.0000% _00 BRK
0.0000% _56 LSR $nn,X
0.0000% _21 AND ($nn,X)
0.0000% _41 EOR ($nn,X)
0.0000% _61 ADC ($nn,X)
0.0000% _B3 LDAX ($nn),Y
0.0000% _E1 SBC ($nn,X)
0.0000% _F8 SED